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11wx

Crystal Structure of ribosomal large subunit pseudouridine synthase D from Neisseria gonorrhoea

Method: X-RAY DIFFRACTION D_max: 101.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11wx
deposition_date	2026-03-16
last_revision	2026-03-25
title	Crystal Structure of ribosomal large subunit pseudouridine synthase D from Neisseria gonorrhoea
keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, Pseudouridine synthase, Neisseria gonorrhoeas, LYASE ;; LYASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	32.00 Å
rg_electron	31.46 Å
i0	106315000.00
molecular_weight	81074.0 kDa
excluded_volume	101310 Å³
envelope_volume	133010 Å³
shell_volume	35595 Å³
envelope_diameter	105.8 Å
shell_rg	38.13 Å
envelope_rg	30.96 Å
shape_rg	31.48 Å
total_rg	31.99 Å
total_atoms	5693
n_residues	739
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	101.7 Å
rg_real	31.93 Å
rg_real_error	0.70 Å
i0_real	1.0630e+08
i0_real_error	1.6340e+06
rg_reciprocal	31.97 Å
i0_reciprocal	106300000.0000
total_estimate	0.9096
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	0
r_peak_primary	— Å
skewness	0.198
kurtosis	-0.635
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	12430000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.963

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Pseudouridine synthase
formula_weight	27928.1 kDa
ec_number	5.4.99.-
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	6164

MAHHHHHHLAFVPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRLKMAAVKFGGKPAVTHVKVLERYLAHSYIECSLGTGRTHQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETVSFEAPIPDDIYHLLSVLRLEAGLDS

Source

organism	Neisseria gonorrhoeae NCCP11945
ncbi_taxonomy_id	521006
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	12

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	471

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6. Citations (1)

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length_a	132.552 Å
length_b	88.011 Å
length_c	101.659 Å
angle_alpha	90.00 °
angle_beta	95.18 °
angle_gamma	90.00 °
z_pdb	12

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.910 Å
resolution_low	44.010 Å
r_factor	0.1692
r_work	0.1679
r_free	0.1931

fit	/app/data/saxs_computation/1w/11wx/11wx.fit
pddf	/app/data/pr_computation/1w/11wx/11wx.pr.out
profile	/app/data/saxs_computation/1w/11wx/11wx.dat